Detailed information of ENSXQXP00000018655.1 in Sanderia malayensis

Genomic Location: ScYm1zk_718:1627209...1630949
NR annotation: no NCBI-NR hit recorded
Species Sanderia malayensis · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0007375 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF17777
all species →
RL10P_insertInsertion domain in 60S ribosomal protein L10PDomainInterproscan
PF00466
all species →
Ribosomal_L10Ribosomal protein L10FamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR043141
all species →
Homologous_superfamilyLarge ribosomal subunit protein uL10-like domain superfamilyInterproscan
IPR040637
all species →
DomainLarge ribosomal subunit protein uL10-like, insertion domainInterproscan
IPR051742
all species →
FamilyRibosomal Assembly Factor uL10Interproscan
IPR033867
all species →
FamilyRibosome assembly factor Mrt4Interproscan
IPR001790
all species →
FamilyLarge ribosomal subunit protein uL10Interproscan
IPR043164
all species →
Homologous_superfamilyLarge ribosomal subunit protein uL10-like, insertion domain superfamilyInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR45841
all species →
MRNA TURNOVER PROTEIN 4 MRTO4Interproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0000956
all species →
Biological Processnuclear-transcribed mRNA catabolic processInterproscan
GO:0003723
all species →
Molecular FunctionRNA bindingInterproscan
GO:0005730
all species →
Cellular ComponentnucleolusInterproscan
GO:0006364
all species →
Biological ProcessrRNA processingInterproscan
GO:0030687
all species →
Cellular Componentpreribosome, large subunit precursorInterproscan
GO:0042273
all species →
Biological Processribosomal large subunit biogenesisInterproscan
GO:0000027
all species →
Biological Processribosomal large subunit assemblyInterproscan

Search by domain instead of by gene. Any accession above (InterPro, Pfam, PANTHER, GO, KEGG) can be used as a query on the Functional Domain Search page, which searches all 148 annotated genomes at once.
 KEGG pathway
KOEnzymeEnzyme IDPathwayMap IDSource
K14815MRT4; mRNA turnover protein 4-Ribosome biogenesisko03009deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Co-expression network

Genes whose expression across the transcriptome samples of Sanderia malayensis tracks this one. Counts are over the whole network; the network view itself draws at most 100 partners per query gene (CNIDO_NET_TOP_K), so a hub gene can show fewer edges than the number below.

No co-expression network has been built for this species, so this gene has no partners to show. Networks are available for the species listed on the Network Analysis page.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Sanderia malayensis, and in which cell types it is a marker. Expression is stored per cell, so the violin plot and the cell-type means are computed in the viewer — open a dataset to see them.

No single-cell dataset has been published for this species. The atlases that do exist are listed in the Cell Atlas.

Epigenetic marks

Chromatin and DNA-methylation data covering this gene. Peak calls are listed per sample with the genomic region the peak falls in; DNA methylation is listed as sample availability only, because those tables are queried by the DNA Methylation page itself.

No epigenomic data has been deposited for this species. The assays that exist across the site are described in the Epigenomic Data module.

What you can do with this gene

Every tool below opens with this gene already entered, so you land on the analysis rather than on an empty form. Links open in a new tab.

AnalysisWhat it doesStatus
Primer designDesign PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.template foundopen →
BLASTSearch this gene’s sequence against the CnidoSite BLAST databases. The query is filled in and the species’ database is preselected — press Run to start.template foundopen →
Expression heatmapDraw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it.no expression matrix
Gene family / orthogroupLook this gene up in the single-copy orthogroups built from the high-quality cnidarian genomes, and see which other species carry an orthologue.open →
Gene set analysisStart a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.open →
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